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Crystal structure of the Sec14 domain of the RhoGEF Kalirin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100 mM sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, 20-25% PEG3350, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.65 53.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.16 α = 81.09 b = 82.42 β = 71.79 c = 83.27 γ = 79.88
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2018-07-09 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-11-16 M SINGLE WAVELENGTH 3 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-02-15 M SINGLE WAVELENGTH 4 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2020-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.195 SSRL BL14-1 2 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9792 SSRL BL12-2 3 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-2 4 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.89 78.64 95.9 0.061 0.063 0.015 1 31.6 18.3 137673 35.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 94 1.294 1.329 0.303 0.907 2.2 19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.89 61.01 137668 6768 95.9 0.196 0.195 0.1922 0.218 0.2181 RANDOM 48.49
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.4352 10.4462 -3.061 3.4146 -1.2604 -0.9794
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.46 t_other_torsion 2.8 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.46 t_other_torsion 2.8 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10652 Nucleic Acid Atoms Solvent Atoms 1412 Heterogen Atoms 35
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHENIX phasing